[gmx-users] What do res_cog, whole_res_cog, and part_res_cog mean in g_select?

Justin Lemkul jalemkul at vt.edu
Tue Dec 18 19:46:51 CET 2012

On 12/18/12 1:29 PM, Yun Shi wrote:
> Hi all,
> I understand a suffix of "com" indicates center of mass, but how about
> "cog" and the prefixes "whole" and "part"?

COG = center of geometry.

 From g_select -select 'help all' you will find:

"3. POSTYPE of ATOM_EXPR calculates the specified positions for the atoms in
ATOM_EXPR. POSTYPE can be atom, res_com, res_cog, mol_com or mol_cog, with an
optional prefix whole_ part_ or dyn_. whole_ calculates the centers for the
whole residue/molecule, even if only part of it is selected. part_ prefix
calculates the centers for the selected atoms, but uses always the same atoms
for the same residue/molecule. The used atoms are determined from the the
largest group allowed by the selection. dyn_ calculates the centers strictly
only for the selected atoms. If no prefix is specified, whole selections
default to part_ and other places default to whole_. The latter is often
desirable to select the same molecules in different tools, while the first is
a compromise between speed (dyn_ positions can be slower to evaluate than
part_) and intuitive behavior."



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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